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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttttcagctttcttaagcaaattcgttcaccaaggaatggtttctctcttccttaagcaaatttgaatattcctttttgaaagtggctctcttccttttcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCAACTCCCACAATGCAGAAAGCCAGCAGTCAGTGTGTGGGCATCATGTTGA

Basic information

species Oryza sativa
transcript LOC_Os01g04660.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04660.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174343_T07 (Zea mays), 3'ss of exon 5
---------------------------------------------------gtttttcagctttcttaagcaaattcgttcaccaaggaatg----gtttctctcttccttaagcaaatttgaatattcctttttgaaagtggc--tctcttccttttcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCAACTCCCACAATGCAGAAAGCCAGCAGTCAGTGTGTGGGCATCATGTTGA
                                                     | |||  | | ||       || |  |  |  |   ||     |||  ||  ||  ||  |  | ||| ||| |||||||| | |  || |  ||| |||||||||  ||| ||||||  ||||||||||||||||||||||||| || || ||||||| ||| || ||  |||| ||| ||| ||| |||||     |||  ||||   ||| 
gttgttcgatctttctcactaagcaaatttgcttccaatagtactgctttaagtgttcgccctgctatcattgatcctctttcttaaacattttctgttgttcattttgtttcgatagtttaaattttccttttcggatatgacggtcttttccttttcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG

upper sequence: LOC_Os01g04660.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174343_T06 (Zea mays), 3'ss of exon 5
gtttttcagctttcttaagcaaattcgttcaccaaggaatggtttctctcttccttaagcaaatttgaatattcctttttgaaagtggc--tctcttccttttcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCAACTCCCACAATGCAGAAAGCCAGCAGTCAGTGTGTGGGCATCATGTTGA
           |  || | |   ||  || | ||     || ||  ||  ||  ||  |  | ||| ||| |||||||| | |  || |  ||| |||||||||  ||| ||||||  ||||||||||||||||||||||||| || || ||||||| ||| || ||  |||| ||| ||| ||| |||||     |||  ||||   ||| 
-----------tcattgatcctctttcttaaacattttctg-ttgttcattttgtttcgatagtttaaattttccttttcggatatgacggtcttttccttttcgccttcagGTTGTAGACCGTATGCATACTTCCATATGCTGGAAGAACTTCAAGCGGCAAATTCAAACAACGCACAAAACCAACAGTCCACAGGTGATCATCGCATTGG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|16575632|gb|BI802928.1|BI802928
EST:     GGCGATGCTCTGTTACTTGCACTTCTTTCCACCTCCATACCATCATCAAG                         GTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA
genomic: GGCGATGCTCTGTTACTTGCACTTCTTTCCACCTCCATACCATCATCAAGgtttttcagc ... tcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA
EST: gi|88845847|gb|CI084577.1|CI084577
EST:     TGCACTTCTTTCCACCTCCATACNATCATCAAG                         GTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA
genomic: TGCACTTCTTTCCACCTCCATACCATCATCAAGgtttttcagc ... tcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA
EST: gi|88262462|gb|CI366236.1|CI366236
EST:     GCTCTG-TAC-TGCACTTCTTTCCACCTCCATACCATCATCAA-                         GTTGGGGACCGTATGCATACTTCCATATGGCTTGAGGAGCTTCAAGTGNCC
genomic: GCTCTGTTACTTGCACTTCTTTCCACCTCCATACCATCATCAAGgtttttcagc ... tcatcttaagGTTGGGGACCGTATGCATACTTCCATAT-GCTTGAGGAGCTTCAAGTGGCC
EST: gi|88266206|gb|CI377108.1|CI377108
EST:     GGCGATGCTCTGTTACTTGCACTTCTTTCCACCTCCATACCATCATCAAG                         GTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA
genomic: GGCGATGCTCTGTTACTTGCACTTCTTTCCACCTCCATACCATCATCAAGgtttttcagc ... tcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcaaatttgaatattcctttttgaaagtggctctcttccttttcatcttaagGTTGGGGACCGTATGCATACTTCCATATGCTTGAGGAGCTTCAAGTGGCCAACTCCCACAATGCAGAAAGCCAGCAGTCAGTGTGTGGGCATCATGTTGA
                              tggctctcttcctttt  CT-rich tract
     aaatttgaatatt  TA-rich tract